If the Witch house basement is created to be inside underground water it will remove water except for the parts that can get waterlogged (stairs, fences etc) this can happen quite a fair amount as the witch basement is a rather large structure.

I've tried a few things to mitigate this, but unfortunately MC code really wants blocks to be placed as waterlogged if the structure is underwater. I might try some other things at some point, or consider taking out some of the stairs

Yeah not sure on the whole process for it. "Illager Invasion" had a similar issue with waterlogging. Not sure how useful this is but this is their commit that fixed the issue: Fuzss/illagerinvasion@42f04f2

I hope this can help, AI is a really great mod and been really fun to play with.

I've implemented a solution that follows Fuzs's strategy, so this should be fixed in the latest versions